Qc reads from init not in qc reads #292

Workflow file for this run

.github/workflows/python-package-conda.yml at 0da5cc4

	name: Combined Workflow

	on:
	# Runs on pushes targeting the default branch
	push:
	branches: ["master"]
	pull_request:
	branches: ["master"]
	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	defaults:
	run:
	shell: bash -el {0} # use default shell

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	build-and-dryrun:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 1

	steps:
	- name: Checkout
	uses: actions/[email protected]

	# - name: Get current month
	# id: date
	# run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}"

	- uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: atlasenv.yml
	environment-name: atlasenv
	# persist on the same month.
	cache-environment-key: atlasenv- #${{ steps.date.outputs.date }}

	- name: Install atlas
	run: \|
	python -m pip install . --no-deps -vv

	- name: Test atlas
	run: \|
	atlas --help
	atlas --version

	- name: test import modules atlas
	run: \|
	python -c "from atlas import utils"

	- name: Dryrun
	run: test/dryrun.sh

	run-qc-and-assembly:
	runs-on: ubuntu-latest
	needs: build-and-dryrun
	env:
	N_THREADS: 2
	MEM: 0.8

	steps:
	- name: Checkout
	uses: actions/[email protected]

	- uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: atlasenv.yml
	environment-name: atlasenv
	cache-environment-key: atlasenv-

	- name: Install atlas
	run: \|
	python -m pip install . --no-deps -vv
	atlas --help

	- name: get example data
	id: get-data
	uses: actions/cache/restore@v3
	with:
	path: test_reads.tar.gz
	key: example-data

	- name: Download test data
	if: steps.get-data.outputs.cache-hit != 'true'
	run: wget --quiet https://zenodo.org/record/3992790/files/test_reads.tar.gz

	- name: cache example data
	if: steps.get-data.outputs.cache-hit != 'true'
	uses: actions/cache/save@v3
	with:
	path: test_reads.tar.gz
	key: ${{ steps.get-data.outputs.cache-primary-key }}

	- name: extract data
	run: \|
	tar -xzf test_reads.tar.gz
	ls -l test_reads

	- name: get conda envs
	id: get-envs
	uses: actions/cache/restore@v3
	with:
	path: databases
	key: conda-envs-assembly

	# - name: upack conda envs
	# if: steps.get-envs.outputs.cache-hit != 'true'
	# run: tar -xzf assembly_conda_envs.tar.gz

	- name: Init
	run: \|
	atlas init "test_reads" --threads "$N_THREADS" --working-dir wd

	- name: Install dependencies for qc and assembly
	if: steps.get-envs.outputs.cache-hit != 'true'
	run: atlas run assembly --conda-create-envs-only -w wd

	- name: List envs
	run: ls -l databases/conda_envs

	- name: Store conda envs
	if: steps.get-envs.outputs.cache-hit != 'true'
	uses: actions/cache/save@v3
	with:
	path: databases
	key: ${{ steps.get-envs.outputs.cache-primary-key }}

	- name: Run QC
	run: \|
	atlas run qc --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd

	- name: Test Assembly
	run: \|
	atlas run assembly --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd

	- name: Store Logs
	uses: actions/upload-artifact@v3
	with:
	name: logs
	path: wd/logs

	- name: Store Sample Logs
	uses: actions/upload-artifact@v3
	with:
	name: sample_logs
	path: wd/sample1/logs

	- name: Store reports
	uses: actions/upload-artifact@v3
	with:
	name: reports
	path: wd/reports

	- name: Cache working dir
	uses: actions/cache/save@v3
	with:
	path: wd
	key: assembly-working-dir

	run-genecatalog:
	runs-on: ubuntu-latest
	needs: [build-and-dryrun, run-qc-and-assembly]
	env:
	N_THREADS: 2
	MEM: 3

	steps:
	- name: Checkout
	uses: actions/[email protected]

	- uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: atlasenv.yml
	environment-name: atlasenv
	cache-environment-key: atlasenv-

	- name: install atlas
	run: \|
	python -m pip install . --no-deps -vv
	atlas --help

	- name: get conda envs
	id: get-envs
	uses: actions/cache/restore@v3
	with:
	path: databases
	key: conda-envs-genecatalog
	restore-keys: \|
	conda-envs-assembly
	conda-envs-

	- name: Restore working dir
	uses: actions/cache/restore@v3
	with:
	path: wd
	key: assembly-working-dir

	- name: dryrun assembly shold need nothing to be done
	run: \|
	ls -l wd
	ls -l databases/conda_envs
	atlas run assembly -w wd -n

	- name: test Genecatalog
	run: \|
	atlas run genecatalog --restart-times=2 --working-dir wd --omit-from combine_egg_nogg_annotations combine_dram_genecatalog_annotations

	- name: Store Logs
	uses: actions/upload-artifact@v3
	with:
	name: logs
	path: wd/logs

	- name: Store Sample Logs
	uses: actions/upload-artifact@v3
	with:
	name: sample_logs
	path: wd/sample1/logs

	- name: Store conda envs
	#if: steps.get-envs.outputs.cache-hit != 'true'
	uses: actions/cache/save@v3
	with:
	path: databases
	key: ${{ steps.get-envs.outputs.cache-primary-key }}

	run-binning:
	runs-on: ubuntu-latest
	needs: [build-and-dryrun, run-qc-and-assembly]
	env:
	MEM: 0.9

	steps:
	- name: Checkout
	uses: actions/[email protected]

	- uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: atlasenv.yml
	environment-name: atlasenv
	cache-environment-key: atlasenv-

	- name: install atlas
	run: \|
	python -m pip install . --no-deps -vv
	atlas --help

	- name: get conda envs
	id: get-envs
	uses: actions/cache/restore@v3
	with:
	path: databases
	key: conda-envs-binning
	restore-keys: \|
	conda-envs-

	- name: Restore working dir
	uses: actions/cache/restore@v3
	with:
	path: wd
	fail-on-cache-miss: true
	key: assembly-working-dir

	- name: dryrun assembly shold need nothing to be done
	run: \|
	ls -l wd
	ls -l databases
	ls -l databases/conda_envs
	atlas run assembly -w wd -n

	- name: test binning
	run: \|
	atlas run binning --restart-times=2 --working-dir wd --omit-from checkm2_download_db --max-mem $MEM &> >(tee wd/logs/atlas_binning.log)

	- name: Store Logs
	uses: actions/upload-artifact@v3
	with:
	name: logs_binning
	path: wd/logs

	- name: Store Sample Logs
	uses: actions/upload-artifact@v3
	with:
	name: sample_logs_binning
	path: wd/sample1/logs

	- name: Store conda envs
	# if: steps.get-envs.outputs.cache-hit != 'true'
	uses: actions/cache/save@v3
	with:
	path: databases
	key: ${{ steps.get-envs.outputs.cache-primary-key }}

	# run-quantify-genomes:
	# runs-on: ubuntu-latest
	# needs: build-and-dryrun

	# steps:
	# - name: Checkout
	# uses: actions/[email protected]

	# - uses: mamba-org/setup-micromamba@v1
	# with:
	# environment-file: atlasenv.yml
	# environment-name: atlasenv
	# cache-environment-key: atlasenv-

	# - name: Install atlas
	# run: \|
	# python -m pip install . --no-deps -vv
	# atlas --help

	# - name: get conda envs
	# id: get-envs
	# uses: actions/cache/restore@v3
	# with:
	# path: databases
	# key: conda-envs-assembly
	# restore-keys: conda-envs-*

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Qc reads from init not in qc reads #292

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Qc reads from init not in qc reads #292

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Workflow file for this run